Ok, sounds like you have done everythung I would have up to this point to try and eliminate all other possiblities. Here is what I would do next. Use a different RX (one with a crystal of either positive of neg. shift and set the Tx to correspond. If you have no more clitches then we have narrowed it down to the RX. If you still get glitches, then you need to send the TX&RX in for re-claibration. It is not uncommon for Rx with multi channel capacity to need service.
There have been several companies that have used 50 channel Tx & Rx (ie: Polk Hobbies). If there is a lot of vibration in your fleet of aricraft, then your chances increase to having radio problems.
There is one more thing that you can check. Pull the Tx case off the back and check the antenna connection.
Maybe thises are helpful suggestions to you. Minie has worked flawlessly.